DNA sequences are an important type of biomedical data that contains many biologically meaningful functional sites such as transcription start site, coding region, translation initiation site, splice site, polyadenylation signal and so on. Our DNA functional site miner (DNAFSMiner) is a web-based software toolbox that aims to predict these functional sites in DNA sequences. There are two software tools. One is called TIS Miner which can be used to predict translation initiation site (TIS) in vertebrate mRNA, cDNA, or DNA sequences. The other is called Poly(A) Signal Miner which can be used to predict polyadenylation (poly(A)) signal in human DNA sequences.

NetCTL predicts CTL epitopes in protein sequences. The current version expands the MHC class I binding predicition to 12 MHC supertypes including the supertypes A26 and B39. The accuracy of the MHC class I peptide binding affinity is significantly improved compared to the earlier version. Also the prediction of proteasonal cleavage has been improved and the updated version has been trained on a set of 886 known MHC class I ligands.

Center for Biological Sequence Analysis, Technical University of Denmark

Splicing Graph Modules (SGM) is a collection of Python modules housed within a Python package to draw splicing graphs (a form of visual representation of several transcript sequences which may exhibit alternative splicing). A web service is available for users to generate splicing graphs using a web browser.

T3SEdb represents such an effort to assemble a comprehensive database of all experimentally determined and putative T3SEs into a web-accessible site. It contains more than 1089 entries of T3SS effector sequence data including primary sequences and functional annotations

GeneNetwork consists of linked resources and analysis tools for systems genetics. It has been designed for the analysis of networks of genes, transcripts, and classic phenotype data sets. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists with genome sequence data and massive transcriptome data sets (expression genetic or eQTL data sets). WebQTL a major module of GeneNetwork that is optimized for fast on-line quantitative trait locus (QTL) analysis of traits that are controlled by combinations of gene variants and environmental factors. WebQTL exploits reference populations of humans (CEPH), mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, barley, and Arabidopsis. Each of these genetic reference populations is accompanied by dense genetic maps used to locate modifier genes that cause downstream differences in expression and phenotypes, including disease susceptibility.